Real-Time Search-Assisted Multiplexed Quantitative Proteomics Reveals System-Wide Translational Regulation of
Hiroko Kozuka-Hata1, Tomoko Hiroki1, Naoaki Miyamura1
1Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
Biomolecules
|June 28, 2023
Summary
This study reveals novel cancer drug targets by analyzing proteome-wide changes in response to suberoylanilide hydroxamic acid (SAHA). The research identifies new peptides from non-canonical short open reading frames (ORFs) and their regulation in cancer cells.
Area of Science:
- Proteomics
- Cancer Biology
- Epigenetics
Background:
- Abnormal histone deacetylase (HDAC) expression is linked to cancer progression, including angiogenesis, metastasis, and chemotherapy resistance.
- Suberoylanilide hydroxamic acid (SAHA) is a known pan-inhibitor of HDACs, investigated for epigenetic cancer therapy.
- Understanding drug-induced proteome dynamics is crucial for developing targeted cancer treatments.
Purpose of the Study:
- To establish a Real-Time Search (RTS)-assisted mass spectrometry platform for quantifying translated products from both canonical and non-canonical open reading frames (ORFs).
- To investigate the proteome-wide regulatory effects of suberoylanilide hydroxamic acid (SAHA) treatment in human cancer cells.
- To identify novel peptides and assess translational regulation in response to drug perturbation.
Main Methods:
- Development of a Real-Time Search (RTS)-assisted mass spectrometric platform for comprehensive proteomic analysis.
- Quantitative proteomic analysis of suberoylanilide hydroxamic acid (SAHA)-treated human HeLa cells.
- Utilized ribosome profiling data to identify peptides from short ORFs in non-coding and other RNA transcripts.
Main Results:
- Identification of approximately 5000 novel peptides encoded by short ORFs within presumed non-coding sequences, lncRNAs, and NMD transcripts.
- Demonstrated dose-dependent, selective translational regulation of a subset of non-canonical short ORFs upon SAHA treatment.
- Observed modulation of key cell cycle and proliferation-related molecules, including UBE2C, CENPF, and PRC1.
Conclusions:
- The study provides the first system-wide landscape of drug-perturbed translational modulation affecting both canonical and non-canonical proteomes in human cancer cells.
- The developed RTS-assisted platform enables deep proteomic profiling, uncovering previously unannotated translated products.
- Findings highlight the potential of targeting non-canonical ORFs and their regulatory pathways in cancer therapy.
Related Concept Videos
02:24Ribosome Profiling
3.6K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.6K
02:28Leaky Scanning
5.2K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.2K
01:33Proteomics
7.5K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
7.5K